- The "Show Me The Monkey" short is shown in its full length. It shows little Stan's erection actually popping up through his pants, the psychiatrist looking at an ad for an expensive boat, telling Stan that it'll take many sessions to cure him of this "imaginary monkey case". Stan asks why the doctor thinks Monkeybone is not real, but is shoved out of the door. Monkeybone then pops out of the case, pushing the doctor out of the skyscraper window. Monkeybone rides the doctor like 'Slim Pickens' in Dr. Strangelove or: How I Learned to Stop Worrying and Love the Bomb (1964), screaming "Yeeha!" as they fall. The doctor is killed, crashing out of frame next to Stan in a splash of blood - but Monkeybone survives. Stan chastises Monkeybone, but Monkeybone tells Stan he doesn't need a psychiatrist. He sticks his finger inside his bottom, telling Stan that it's the best way to stop sucking his thumb (it's references later in the regular version with the Monkeybone toy which has ITS thumb in its bottom). Stan tells him to "get back in the pack!" (which Stu says twice to Monkeybone later in the regular version of the film.)
- After the car crashes due to the inflated Monkeybone boat, Stu and Julie exit the car. Herb runs up to them, and is inspired with an idea for Monkeybone car air bags. Stu is incensed that Herb is calling a merchandising department instead of reporting the accident. Julie tells Stu to calm down, and use a pay phone to report the accident to the authorities. Unfortunately, a pipe which had been loosened by the crash falls on the booth, putting Stu in a coma.
- Stu finds a Visible Man and Visible Woman in his psychological baggage. When arriving at Coma Town, there are creatures that first meet Stu rummage through his baggage, looking at a training bra and other odd items. Stu also tries to talk to coma cases on line for the Morpheum Theater, and meets other creatures from his nightmares, like a western cowboy centaur. A bizarre turtle, instead of Joe Camel, asks Stu for a smoke. A three-headed Devil compliments Stu's work, and asks for Stu's autograph - in blood, of course.
- Stu first meets Moneybone when the elephant piano player approaches the bar, and Moneybone pops out of his knapsack. There are two versions of this: in one version, Monkeybone announces, "Fee fi fo fum, Something smells like..." and then pulls his thumb out of his bottom. The other version, he says, "Just kidding folks! Drinks on the house," then adds, nodding at Stu, "On him, of course." In both versions, he then kisses him and says, "Hiya, Boss", as he does in the regular version.
- In an extended version of the "Love Is A Drug" scene, Stu spies his macabre paintings on display at Hypnos' party. Monkeybone tells him that he finds them disgusting and repelling. Stu gets angry, and tells him that the paintings are art, and that Monkeybone is only a doodle. The full version of "Love Is A Drug" is played, with more dancing by the town's inhabitants.
- An extended scene with Hypnos. Monkeybone gets drunk on Hypnos' wine, annoying Stu. The bee Hypnos is laying down with flies away. Hypnos reveals that he is Death's brother. (Interesting to note Stu is never told that Hypnos is Death's brother at anytime except for the extended version of the scene, yet reveals this knowledge when being tortured by Death.) Stu decides to go to the Land of Death on his own, but Monkeybone, despite his fear, desperately convinces Stu to take him along, telling him "You gotta take me with you!" At that point, one of the Reapers comes to the party, and claims a party guest, Lulu, after she hits on him. This is the same dead girl Stu and Monkeybone follow in the regular version.
- There is a brief scene in which Death's Helper complains that "no one understands I was born to dance", then goes through "Death's Door" to help Death process souls.
- Monkeybone in Stu's body, is shaving off the beard he had in a coma, when Kimmy comes in, apologizing for wanting to pull the plug. She tells him that if there is anything she could do to make it up to him, she would do it. Monkeybone Stu closes the hospital room's door, tells Kimmy that she's awfully attractive, and starts dancing with her suggestively, exclaiming, "ALL ABOARD! BABY GOT A BIG CABOOSE!" Scene cuts to Julie walking toward the room, while Stu can be heard crowing, "GET ON THE BOOTY TRAIN!" A second later, Stu screams "Ow!" after being punched by Kimmy then kicked in the groin, who comes out the door looking flustered by her brother's sexual advances. Stu, still clutching his groin, says "nothing happened".
- The scene in which the "Little Jack Horner" Monkeybone doll is extended, with the other executives actually getting on the table and rubbing bottoms with Monkeybone Stu. After they leave, Monkeybone Stu tells Herb that at the Monkeybone benefit that they should have a giant piñata full of Monkeybone dolls. As Stu continues to behave strangely, taking one of the Burger God reps white jackets, Herb is asked if Stu has been improving since the accident. Herb gleefully says, "Has he ever!"
- The alternate ending has instead of the Monkeybone cartoon ending where Herb tells people to take off their clothes, Death pays Hypnos a visit, who is packing his bags. Death grabs Hypnos out of his tower, and Downtown closes for the night.